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    <title>Variant Annotation</title>
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    <h1>
      <strong>Variant Annotation:<br> pSEVA uses UCSC database, PolyPhen and SIFT for Variant Annotation. </strong>
    </h1>
    <hr>


    <p>
      <strong>SAMtools</strong>
    </p>
    
    <p>
    SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
    </p>
    <p>
    Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] 
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      <p>
        <strong>First, view Options</strong>
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       <p>
        <input type="checkbox" name="view_bam"/>Output in the BAM format
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       <p>
        <input type="checkbox" name="view_uncompressed"/>Output uncompressed BAM
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       <p>
        <input type="checkbox" name="view_header"/>Include the header in the output
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       <p>
        <input type="checkbox" name="view_headeronly"/>Output the header only
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       <p>
        <input type="checkbox" name="view_input_sam"/>Input is in SAM
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      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;The order of the reference sequences &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="view_ref_order" />
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      <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Output file &nbsp;&nbsp;<input type="text" size="10" name="view_output" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Only output alignments with all bits in INT present in the FLAG field &nbsp;&nbsp; <input type="text" size="10" name="view_flag" value="0"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Skip alignments with bits present in INT &nbsp;&nbsp; <input type="text" size="10" name="view_skip_F" value="0"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Skip alignments with MAPQ smaller than INT &nbsp;&nbsp; <input type="text" size="10" name="view_skip_q" value="0"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Only output reads in library &nbsp;&nbsp; <input type="text" size="10" name="view_library" value="null"/>
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Only output reads in read group &nbsp;&nbsp; <input type="text" size="10" name="view_read_group" value="null"/>
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      <p>
        <strong>Second, sort Options</strong>
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       <p>
        <input type="checkbox" name="sort_name"/>Sort by read names
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Maximum required memory &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="sort_memory" value="500000000"/>
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      <p>
        <strong>Third, Pileup Options</strong>
      </p>
      
       <p>
        <input type="checkbox" name="pileup_mapping_quality"/>Print the mapping quality as the last column
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       <p>
        <input type="checkbox" name="pileup_SAM"/>The input file is in SAM
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       <p>
        <input type="checkbox" name="pileup_indels"/>Only output plileup lines containing indels
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;The reference sequence in the FASTA format &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="pileup_ref" />
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        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;Cap mapping quality &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="pileup_Cap_mapqual" value="60" />
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       <p>
        &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;List of reference names and sequence length &nbsp;&nbsp;&nbsp;<input type="text" size="10" name="pileup_ref_index" />
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